Hi, I'm not sure if this is a GEF issue...
but the only GEF reference help I can find online is for the galileo eclipse. My indigo doesn't even mention GEF on help, but it is installed and running. What are you doing? is there some separated download for the most updated reference help?

By the way, it is not the only missing help on indigo...
Downloaded the last 3.7.1 SDK, but it seems that the SDK does not have help plugin anymore.